Initiation of DNA replication is a major control point in the mammalian cell cycle, and the point of action of many gene products that are mis-regulated in cancer (Hanahan and Weinberg, 2000). The initiation process involves assembly of pre-replication complex proteins, which include the origin recognition complex (ORC), Cdc6, Cdt1 and Mcm proteins, at replication origins during G1 phase of the cell cycle. This is followed by the action of a second group of proteins, which facilitate loading of DNA polymerases and their accessory factors including PCNA, and the transition to S phase. The initiation process is regulated by cyclin-dependent protein kinase 2 (Cdk2), Cdc7-dbf4 and the Cdt1 inhibitor geminin (for review see Bell and Dutta, 2002). In the nucleus of S phase cells, replication forks cluster together to form hundreds of replication ‘foci’ or factories (Cook, 1999). Replication factories appear to be linked to a structural framework within the nucleus, however the nature of the molecules that form the link and their role in replication fork activity remains unclear.
Identification of proteins involved in eukaryotic DNA replication and analysis of the basic pathways that regulate their activity during the cell cycle has been driven largely by yeast genetics. These proteins and pathways are generally conserved from yeast to man. However, in multi-cellular organisms that differentiate down diverse developmental pathways, additional layers of complexity are being uncovered. For example, in vertebrates several proteins involved in neuronal differentiation also regulate the G1-S phase transition (Ohnuma et al., 2001). These include the cdk inhibitor p21CIP1/WAF1/SDI1 which has been implicated in oligodendrocyte differentiation following growth arrest (Zezula et al., 2001), and in the terminal differentiation of other cell types (Parker et al., 1995).
Initiation of DNA replication can be reconstituted in vitro with isolated nuclei and cytosolic extracts from mammalian cells (Krude, 2000; Krude et al., 1997; Laman et al., 2001; Stoeber et al., 1998). Furthermore, using recombinant Cdk2 complexed with either cyclins E or A, replication complex assembly and activation of DNA synthesis can be reconstituted independently (Coverley et al., 2002). We have studied the activation step, catalyzed in vitro by cyclin A-cdk2, and shown that a relatively unstudied protein, p21-Cip1 interacting zinc-finger protein (Ciz1) functions during this stage of the initiation process. Human Ciz1 was previously identified using a modified yeast two-hybrid screen with cyclin E-p21, and biochemical analysis supported an interaction with p21 (Mitsui et al., 1999). A potential role in transcription was proposed but not demonstrated, and no other function was assigned to Ciz1. More recently the Ciz1 gene was isolated from a human medulloblastoma derived cDNA library using an in vivo tumorigenesis model (Warder and Keherly, 2003). Our analysis shows for the first time that Ciz1 plays a positive role in initiation of DNA replication.
A number of changes to chromatin bound proteins occur when DNA synthesis is activated in vitro by recombinant cyclin A-cdk2. The present invention relates to the finding that a cdc6-related antigen, p85, correlates with the initiation of DNA replication and is regulated by cyclin A-cdk2. The protein was cloned from a mouse embryo library and identified as mouse Ciz1.
In vitro analysis has shown that Ciz1 protein positively regulates initiation of DNA replication and that its activity is modulated by cdk phosphorylation at threonine 191/2, linking it to the cdk-dependent pathways that control initiation. The embryonic form mouse Ciz1 is alternately spliced, compared to predicted and somatic forms. Human Ciz1 is also alternately spliced, with variability in the same exons as mouse Ciz1. It has been found that recombinant embryonic form Ciz1 promotes initiation of mammalian DNA replication and that pediatric cancers express ‘embryonic-like’ forms of Ciz1. Without wishing to be held to one theory, the inventors propose that Ciz1 mis-splicing produces embryonic-like forms of Ciz1 at inappropriate times in development. This promotes inappropriately regulated DNA replication and contributes to formation or progression of cancer cell lineages.
A number of techniques have been developed in recent years which purport to specifically ablate genes and/or gene products. For example, the use of anti-sense nucleic acid molecules to bind to and thereby block or inactivate target mRNA molecules is an effective means to inhibit the production of gene products.
A much more recent technique to specifically ablate gene function is through the introduction of double stranded RNA, also referred to as inhibitory RNA (RNAi), into a cell which results in the destruction of mRNA complementary to the sequence included in the RNAi molecule. The RNAi molecule comprises two complementary strands of RNA (a sense strand and an antisense strand) annealed to each other to form a double stranded RNA molecule. The RNAi molecule is typically derived from the exonic or coding sequence of the gene which is to be ablated.
Nucleic acids and proteins have both a linear sequence structure, as defined by their base or amino acid sequence, and also a three dimensional structure which in part is determined by the linear sequence and also the environment in which these molecules are located. Conventional therapeutic molecules are small molecules, for example, peptides, polypeptides, or antibodies, which bind target molecules to produce an agonistic or antagonistic effect. It has become apparent that nucleic acid molecules also have potential with respect to providing agents with the requisite binding properties which may have therapeutic utility. These nucleic acid molecules are typically referred to as aptamers.
Aptamers are small, usually stabilized, nucleic acid molecules which comprise a binding domain for a target molecule.
Aptamers may comprise at least one modified nucleotide base. The term “modified nucleotide base” encompasses nucleotides with a covalently modified base and/or sugar. For example, modified nucleotides include nucleotides having sugars which are covalently attached to low molecular weight organic groups other than a hydroxyl group at the 3′ position and other than a phosphate group at the 5′ position. Thus modified nucleotides may also include 2′ substituted sugars such as 2′-O-methyl-; 2-O-alkyl; 2-O-allyl; 2′-S-alkyl; 2′-S-allyl; 2′-fluoro-; 2′-halo or 2; azido-ribose, carbocyclic sugar analogues a-anomeric sugars; epimeric sugars such as arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars, and sedoheptulose.
Modified nucleotides are known in the art and include by example and not by way of limitation; alkylated purines and/or pyrimidines; acylated purines and/or pyrimidines; or other heterocycles.
These classes of pyrimidines and purines are known in the art and include, pseudoisocytosine; N4,N4-ethanocytosine; 8-hydroxy-N6-methyladenine; 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil; 5-fluorouracil; 5-bromouracil; 5-carboxymethylaminomethyl-2-thiouracil; 5-carboxymethylaminomethyl uracil; dihydrouracil; inosine; N6-isopentyl-adenine; 1-methyladenine; 1-methylpseudouracil; 1-methylguanine; 2,2-dimethylguanine; 2-methyladenine; 2-methylguanine; 3-methylcytosine; 5-methylcytosine; N6-methyladenine; 7-methylguanine; 5-methylaminomethyl uracil; 5-methoxy amino methyl-2-thiouracil; 3-D-mannosylqueosine; 5-methoxycarbonylmethyluracil; 5-methoxyuracil; 2 methylthio-N6-isopentenyladenine; uracil-5-oxyacetic acid methyl ester; psueouracil; 2-thiocytosine; 5-methyl-2 thiouracil, 2-thiouracil; 4-thiouracil; 5-methyluracil; N-uracil-5-oxyacetic acid methylester, uracil 5-oxyacetic acid; queosine; 2-thiocytosine; 5-propyluracil; 5-propylcytosine; 5-ethyluracil; 5-ethylcytosine; 5-butyluracil; 5-pentyluracil; 5-pentylcytosine; and 2,6,-diaminopurine; methylpseudouracil; 1-methylguanine; 1-methylcytosine;
Aptamers may be synthesized using conventional phosphodiester linked nucleotides using standard solid or solution phase synthesis techniques which are known in the art. Linkages between nucleotides may use alternative linking molecules. For example, linking groups of the formula P(O)S, (thioate); P(S)S, (dithioate); P(O)NR′2; P(O)R′; P(O)OR6; CO; or CONR′2 wherein R is H (or a salt) or alkyl (1-12C) and R6 is alkyl (1-9C) is joined to adjacent nucleotides through —O— or —S—.
Other techniques which purport to specifically ablate genes and/or gene products focus on modulating the function or interfering with the activity of protein molecules. Proteins can be targeted by chemical inhibitors drawn, for example, from existing small molecule libraries.
Antibodies, preferably monoclonal, can be raised for example in mice or rats against different protein isoforms. Antibodies, also known as immunoglobulins, are protein molecules which have specificity for foreign molecules (antigens). Immunoglobulins (Ig) are a class of structurally related proteins consisting of two pairs of polypeptide chains, one pair of light (L) (low molecular weight) chain (κ or λ), and one pair of heavy (H) chains (γ, α, μ, δ and ε), all four linked together by disulphide bonds. Both H and L chains have regions that contribute to the binding of antigen and that are highly variable from one Ig molecule to another. In addition, H and L chains contain regions that are non-variable or constant.
The L chains consist of two domains. The carboxy-terminal domain is essentially identical among L chains of a given type and is referred to as the “constant” (C) region. The amino terminal domain varies from one L chain to anther and contributes to the binding site of the antibody. Because of its variability, it is referred to as the “variable” (V) region.
The H chains of Ig molecules are of several classes, α, μ, σ, α and γ (of which there are several sub-classes). An assembled Ig molecule consisting of one or more units of two identical H and L chains, derives its name from the H chain that it possesses. Thus, there are five Ig isotypes: IgA, IgM, IgD, IgE and IgG (with four sub-classes based on the differences in the H chains, i.e., IgG1, IgG2, IgG3 and IgG4). Further detail regarding antibody structure and their various functions can be found in, Using Antibodies: A laboratory manual, Cold Spring Harbour Laboratory Press.
Chimeric antibodies are recombinant antibodies in which all of the V-regions of a mouse or rat antibody are combined with human antibody C-regions. Humanized antibodies are recombinant hybrid antibodies which fuse the complimentarity determining regions from a rodent antibody V-region with the framework regions from the human antibody V-regions. The C-regions from the human antibody are also used. The complimentarity determining regions (CDRs) are the regions within the N-terminal domain of both the heavy and light chain of the antibody to where the majority of the variation of the V-region is restricted. These regions form loops at the surface of the antibody molecule. These loops provide the binding surface between the antibody and antigen.
Antibodies from non-human animals provoke an immune response to the foreign antibody and its removal from the circulation. Both chimeric and humanized antibodies have reduced antigenicity when injected to a human subject because there is a reduced amount of rodent (i.e. foreign) antibody within the recombinant hybrid antibody, while the human antibody regions do not illicit an immune response. This results in a weaker immune response and a decrease in the clearance of the antibody. This is clearly desirable when using therapeutic antibodies in the treatment of human diseases. Humanized antibodies are designed to have less “foreign” antibody regions and are therefore thought to be less immunogenic than chimeric antibodies.
Other techniques for targeting at the protein level include the use of randomly generated peptides that specifically bind to proteins, and any other molecules which bind to proteins or protein variants and modify the function thereof.
Understanding the DNA replication process is of prime concern in the field of cancer therapy. It is known that cancer cells can become resistant to chemotherapeutic agents and can evade detection by the immune system. There is an on going need to identify targets for cancer therapy so that new agents can be identified. The DNA replication process represents a prime target for drug intervention in cancer therapy. There is a need to identify gene products which modulate DNA replication and which contribute to formation or progression of cancer cell lineages, and to develop agents that affect their function.